Yeah, pretty positive a refresh does overwrite the templates. My guess would be there's some confusion about the snapshot date/time, timing of file edits, timing of template edits, file permission changes, multiple sandboxes, or the actual order that all this happened in. Speaking from my own personal experience, it's real easy to get mixed up with the timing of changes, particularly when a sandbox refresh takes a while to get activated and you're working on things in the interim.